[Bioc-devel] ExperimentHub::GSE62944 outdated

[Ludwig Geistlinger]

Hi,

I would like to do some analysis on the TCGA data as provided in
ExperimentHub's GSE62944 ExpressionSet.

The Description of the dataset reads:

"TCGA re-processed RNA-Seq data from 9264 Tumor Samples and 741 normal
samples across 24 cancer types"

However, when loading the dataset via

> eh <- ExperimentHub()
> query(eh , "GSE62944")
> tcga_data <- eh[["EH1"]]

and counting the samples

> dim(tcga_data)
Features  Samples
   23368 7706

as well as the cancer types

> length(table(pData(tcga_data)[,"CancerType"]))

results in the observed discrepancies with the above description,
indicating that this is an outdated version of the dataset.

Is it possible to

(1) update it accordingly
(2) include a varLabel, i.e. pData column indicating whether this is a
tumor or an adjacent normal sample for the respective cancer type.

That would be great!

Thx & Best,
Ludwig

-- 
Dr. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de

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[Bioc-devel] Workflows for Bioconductor channel at F1000R

[Wolfgang Huber]

Susan

I’m giving my reply via the Bioconductor mailing list to also include the 
others, both for input from the core team, and for information of other 
workflow authors.

The preferred approach is to host a live version of the workflow on 
http://www.bioconductor.org/help/workflows/ - with the obvious advantages of 
easy installation for users (e.g. 
http://www.bioconductor.org/help/workflows/rnaseqGene) and continuous testing.

The .Rmds are (and can be maintained by the authors) at 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows . The 
Bioconductor project is moving from subversion to github, maybe Martin or 
someone can outline the ramifications, if any, for authors.

To get the document from there into F1000R, Mike Love made notes: 
https://docs.google.com/document/d/1SC1Z6TS6eepNelu4Eyng7cdbJBMXzZZoMOzfLEYe0LE/edit
The main effort being in manually uploading the figures to Overleaf​ and in 
manually adding figure captions. I wish this could be further automated.

Kind regards
Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
http://www.huber.embl.de


> On 1 Jun 2016, at 16:52, Susan Holmes  wrote:
> 
> Hi there,
> So I a managed to get our workflow paper in before midnight last night (it is 
> quite long, mainly because of the pictures), I am in touch with their office 
> through
> someone called Paola and she says they prefer a GitHub repository,
> did you do that? Is there a preferred directory/document structure?
> Should I make a Bioconductor Workflow like document to publish alongside?
> 
> 
> Best
> Susan
> 
> 
> Susan Holmes
> Professor, Statistics and BioX
> John Henry Samter University Fellow
> coDirector, Math Comp Sci
> 102, Sequoia Hall,  
> 390 Serra Mall,
> Stanford
> http://www-stat.stanford.edu/~susan/
> 
> 

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